Biomarkers for predicting relapse in multiple sclerosis

ABSTRACT

Methods of determining relapse in subjects having relapsing-remitting multiple sclerosis (RRMS) and predicting their response to glatiramer acetate (GA) using the biomarkers SIRT1, RGC-32, FasL and IL-21 are presented.

BACKGROUND OF INVENTION

Multiple sclerosis (MS) is a demyelinating disease characterized bychronic inflammation of the central nervous system in which many factors(genetic and environmental) may act together to influence diseasesusceptibility and progression (Frohman et al., 2006; Keegan andNoseworthy, 2002). While a large body of work has enhanced anunderstanding of the fundamental nature of MS, basic research into itsetiology, pathophysiology, and treatment faces enormous challenges, andthis may in part be due to the great variability in the clinicalpresentation and course of MS (Compston and Coles, 2008; Frohman et al.,2006; Keegan and Noseworthy, 2002).

Relapsing-remitting multiple sclerosis (RRMS) is one of the two mainforms of the disease, the other being primary-progressive multiplesclerosis (PPMS). RRMS is characterized by periods of worseningneurologic function (Lublin et al., 2014; Polman et al., 2011). Theseperiods, termed relapses or flare-ups, are followed by partial orcomplete recovery periods (remissions), during which symptoms improvepartially or completely, and there is no apparent disease progression.RRMS is the most common disease course at the time of diagnosis (Lublinet al., 2014; Polman et al., 2011). Approximately 85 percent of peopleare initially diagnosed with RRMS, compared to 10-15 percent withprogressive forms of the disease (Lublin et al., 2014; Polman et al.,2011). RRMS is defined by inflammatory attacks on myelin, as well as thenerve fibers themselves (Lublin et al., 2014; Polman et al., 2011).During these inflammatory attacks, activated immune cells cause small,localized areas of damage which produce the symptoms of MS (Lublin etal., 2014; Polman et al., 2011). Because the location of the damage isso variable, no two people have exactly the same symptoms.

While RRMS is defined by attacks of inflammation (relapses) in thecentral nervous system (CNS), the progressive form of MS involves muchless of this type of inflammation. Subjects with RRMS tend to have morebrain lesions, also called plaques or scars, detectable via magneticresonance imaging (MRI) scans, and these lesions contain moreinflammatory cells. Subjects with PPMS tend to have more spinal cordlesions, which contain fewer inflammatory cells.

A subject is diagnosed as having RRMS when test results provide evidenceof at least two separate areas of damage to the myelin in the CNS thathave occurred at different points in time (nationalmssociety.org). Teststhat may be used to determine whether there is relevant damage to myelinin a subject include magnetic resonance imaging (MRI), visual evokedpotential (VEP) testing, and analysis of the cerebrospinal fluid(nationalmssociety.org).

These tests have drawbacks, including pain, risks and costs. Forexample, a brain MRI is an expensive test that is hard to tolerate byclaustrophobic patients. In addition, identification of active lesionson a brain Mill requires the administration of the gadolinium to asubject, which poses significant risks of allergic reactions andgadolinium-associated nephrogenic systemic fibrosis (Grobner T., 2006;Hellman, R., 2011). Indeed, gadolinium associated nephrogenic systemicfibrosis is a systemic, sometimes fatal (mortality rate up to 30%),disabling disease, mimicking scleroderma (Grobner T., 2006; Hellman, R.,2011).

The development of additional means for diagnosing a subject as havingRRMS or determining whether a subject already diagnosed with MS isexperiencing a relapse will greatly aid clinicians in quickly andaccurately prescribing appropriate treatment. The present invention isdirected to these and other important goals.

BRIEF SUMMARY OF INVENTION

The present invention is generally directed to the use of sirtuin 1(SIRT1), RGC-32, FasL and IL-21 as biomarkers in determining whether asubject previously diagnosed as having relapsing-remitting multiplesclerosis (RRMS) is undergoing a relapse of the disease and topredicting whether a subject having RRMA will respond to treatment withglatiramer acetate (GA).

The invention is derived from the investigations conducted by theinventors and presented herein. As discussed in detail below, theinventors studied the expression of several biomarkers, including SIRT1,RGC-32, FasL and IL-21, in RRMS patients undergoing relapse (relapseRRMS) and compared expression levels to those of healthy controls andRRMS patients not experiencing relapse (stable RRMS). Levels of SIRT1,RGC-32 and FasL mRNA and protein were found to be significantly reducedin RRMS patients with relapse as compared to control patients, whilelevels of IL-21 mRNA and protein were found to be increased. Thus, itwas found that changes in the expression levels of these four moleculescould be used as markers of disease activity in patients with RRMS.

In a first embodiment, the invention is generally drawn to methods fordetermining whether a subject having relapsing-remitting multiplesclerosis (RRMS) is undergoing relapse of the disease by monitoringlevels of mRNA expression of certain biomarkers. In particular, theinvention is drawn to methods for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising

(i) determining mRNA expression levels for one or more biomarkersselected from the group consisting of SIRT1, RGC-32, FasL and IL-21 in apopulation of cells,

(ii) determining mRNA expression levels for L13 in the same populationof cells, and

(iii) calculating a ratio of biomarker mRNA expression to L13 mRNAexpression,

wherein when the biomarker is SIRT1 and the SIRT1/L13 ratio is<3.06±10%, the subject is determined to be undergoing relapse,wherein when the biomarker is RGC-32 and the RGC-32/L13 ratio is<1.27±10%, the subject is determined to be undergoing relapse,wherein when the biomarker is FasL and the FasL/L13 ratio is <52.6±10%,the subject is determined to be undergoing relapse, andwherein when the biomarker is IL-21 and the IL-21/L13 ratiois >16.9±10%, the subject is determined to be undergoing relapse.

In certain aspects of this embodiment, when the biomarker is SIRT1, theSIRT1/L13 ratio is about <3.06. In certain aspects of this embodiment,when biomarker is RGC-32, the RGC-32/L13 ratio is about <1.27. Incertain aspects of this embodiment, when the biomarker is FasL, theFasL/L13 ratio is about <52.6. In certain aspects of this embodiment,when the biomarker is IL-21, the IL-21/L13 ratio is about >16.9.

In certain aspects of this embodiment, mRNA expression levels for one,two, three or all of the four biomarkers is determined.

In certain aspects of this embodiment, when the subject is determined tobe undergoing relapse, the method further comprises administering atherapeutically effective amount of a treatment for RRMS to the subject.The treatment may be, for example, glatiramer acetate (GA),beta-interferons, teriflunomide, fingolimod, dimethyl fumarate, andnatalizumab.

In a second embodiment, the invention is generally drawn to methods fordetermining whether a subject having relapsing-remitting multiplesclerosis (RRMS) is undergoing relapse of the disease by monitoringlevels of protein expression of certain biomarkers. In particular, theinvention is drawn to methods for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising

(i) determining protein expression levels for SIRT1 in a population ofcells,

(ii) determining protein expression levels for L13 in the samepopulation of cells, and

(iii) calculating a ratio of SIRT1 protein expression to L13 proteinexpression,

wherein when the SIRT1/L13 ratio is <0.645±10%, the subject isdetermined to be undergoing relapse.

In certain aspects of this embodiment, the SIRT1/L13 ratio is about<0.645.

In certain aspects of this embodiment, when the subject is determined tobe undergoing relapse, the method further comprises administering atherapeutically effective amount of a treatment for RRMS to the subject.The treatment may be, for example, glatiramer acetate (GA),beta-interferons, teriflunomide, fingolimod, dimethyl fumarate, andnatalizumab.

In a third embodiment, the invention is generally drawn to methods fordetermining whether a subject having relapsing-remitting multiplesclerosis (RRMS) will respond to treatment with glatiramer acetate (GA).In particular, the invention is drawn to methods for determining whethera subject having relapsing-remitting multiple sclerosis (RRMS) willrespond to treatment with GA, comprising

(i) determining mRNA expression levels for one or more biomarkersselected from the group consisting of SIRT1, RGC-32, FasL and IL-21 in apopulation of cells,

(ii) determining mRNA expression levels for L13 in the same populationof cells, and

(iii) calculating a ratio of biomarker mRNA expression to L13 mRNAexpression,

wherein when the biomarker is SIRT1 and the SIRT1/L13 ratiois >4.33±10%, it is determined that the subject will respond totreatment with GA,wherein when the biomarker is RGC-32 and the RGC-32/L13 ratiois >2.52±10%, it is determined that the subject will respond totreatment with GA,wherein when the biomarker is FasL and the FasL/L13 ratio is >85.4±10%,it is determined that the subject will respond to treatment with GA, andwherein when the biomarker is IL-21 and the IL-21/L13 ratio is<11.9±10%, it is determined that the subject will respond to treatmentwith GA.

In certain aspects of this embodiment, when the biomarker is SIRT1, theSIRT1/L13 ratio is about >4.33. In certain aspects of this embodiment,when biomarker is RGC-32, the RGC-32/L13 ratio is about >2.52. Incertain aspects of this embodiment, when the biomarker is FasL, theFasL/L13 ratio is about >85.4. In certain aspects of this embodiment,when the biomarker is IL-21, the IL-21/L13 ratio is about <11.9.

In certain aspects of this embodiment, mRNA expression levels for one,two, three or all of the four biomarkers is determined.

In certain aspects of this embodiment, when it is determined that thesubject will respond to treatment with GA, the method further comprisesadministering a therapeutically effective amount of GA to the subject.When it is determined that the subject will not respond to treatmentwith GA, the method further comprises administering a therapeuticallyeffective amount of another, non-GA treatment suitable for RRMSincluding, but not limited to, beta-interferons, teriflunomide,fingolimod, dimethyl fumarate, and natalizumab.

In each of the embodiments and aspects of the invention, the populationof cells may be, but is not limited to, peripheral blood mononuclearcells (PBMCs), CD4+ T cells, CD8+ T cells, MAB328+ cells, GFAP+ cells,leukocytes, monocytes, glial cells, dendritic cells, and neurons.

The foregoing has outlined rather broadly the features and technicaladvantages of the present invention in order that the detaileddescription of the invention that follows may be better understood.Additional features and advantages of the invention will be describedherein, which form the subject of the claims of the invention. It shouldbe appreciated by those skilled in the art that any conception andspecific embodiment disclosed herein may be readily utilized as a basisfor modifying or designing other structures for carrying out the samepurposes of the present invention. It should also be realized by thoseskilled in the art that such equivalent constructions do not depart fromthe spirit and scope of the invention as set forth in the appendedclaims. The novel features which are believed to be characteristic ofthe invention, both as to its organization and method of operation,together with further objects and advantages will be better understoodfrom the following description when considered in connection with theaccompanying figures. It is to be expressly understood, however, thatany description, figure, example, etc. is provided for the purpose ofillustration and description only and is by no means intended to definethe limits the invention.

BRIEF DESCRIPTION OF DRAWINGS

FIGS. 1A-1D. Immunohistochemical staining for SIRT1 and phosphorylatedSIRT1 (p-SIRT1) in MS brains. SIRT1 and phosphorylated SIRT1 (“p-SIRT1”)were localized in MS brain by immunostaining. (FIG. 1A) Perivasculardeposits of SIRT1 on inflammatory cells in MS plaque (arrows). (FIG. 1B)Parenchymal deposits of SIRT1 in normal adjacent gray matter; somepositive cells have morphology suggestive of glial cells (arrows). (FIG.1C) Perivascular deposits of p-SIRT1 on perivascular cells in an MSplaque. P-SIRT1 deposits are localized to the nucleus (arrows).Hematoxylin was not used for counterstaining in this experiment. (FIG.1D) Control for the immunoperoxidase reaction. FIGS. 1A-1D: originalmagnification, ×400.

FIGS. 2A-2D. Immunohistochemical staining for HDAC3 and phosphorylatedHDAC3 (p-HDAC3) in MS brains. HDAC3 and phosphorylated HDAC3 (“p-HDAC3”)were localized in MS brain by immunostaining. (FIG. 2A) Perivasculardeposits of HDAC3 on inflammatory cells in an MS plaque (arrows). (FIG.2B) Parenchymal deposits of HDAC3, which are localized to the nucleus(arrows). Hematoxylin was not used for counterstaining in thisexperiment. (FIG. 2C) Perivascular deposits of p-HDAC3 on inflammatorycells in normal adjacent white matter. Some positive cells havemorphology suggestive of glial cells (arrows). pHDAC3 was localized bothin the cytoplasm and in the nucleus. (FIG. 2D) Control for theimmunoperoxidase reaction. FIGS. 2A-2D: original magnification, ×400.

FIGS. 3A-3F. Co-localization of SIRT1 with cells positive for CD4, CD68,GFAP, and MAB328 in MS brains. FIG. 3A, FIG. 3B. SIRT1-expressing cellswere co-localized by double staining. (FIG. 3A) By double-staining, someof the SIRT1-positive cells are seen to be co-localized with CD4 T cellsin an MS plaque (arrows and insert). Not all the SIRT1-positive cells inparenchymal areas express CD4. (FIG. 3B) SIRT1-positive cells are seento be co-localized with CD68 in an MS plaque (arrows). (FIG. 3C)SIRT1-positive cells are also co-localized with OLG in an MS plaque(arrows). Almost all OLG have nuclear deposits of SIRT1. (FIG. 3D)SIRT1-positive cells are co-localized with GFAP in an MS plaque(arrows). (FIG. 3E) Staining of the same area as in FIGS. 3A-3D formyelin/OLG using MAB328 shows significant demyelination in an MS plaque.(FIG. 3F) Control for the immunoperoxidase reaction. Originalmagnification: FIGS. 3A-3D (×400); FIG. 3E (×100); FIG. 3F (×400);Inserts, (×1000).

FIGS. 4A-4C. Expression of SIRT1 and HDAC3 in MS patients and controls.The expression of SIRT1 and HDAC3 mRNA was measured by real-time PCR andexpressed as a ratio to L13. SIRT1 protein was measured by westernblotting. (FIG. 4A) A statistically significant decrease in SIRT1 wasfound in patients with relapse when compared to controls (p<0.04). (FIG.4B) Levels of HDAC3 mRNA in MS patients were similar to those incontrols. (FIG. 4C) SIRT1 protein expression was significantly decreasedin the MS patients with relapses when compared to both stable MSpatients and controls.

FIGS. 5A-5D. Expression of histone H3K9ac and H3K9me2 in MS patients andcontrols. Acetylation and methylation of histone H3 at lysine 9 wasassessed by western blotting using specific antibodies against H3K9acand H3K9me2. (FIG. 5A) An example of a western blot relevant to theexpression of histone H3K9ac (upper panel). Higher levels of H3K9ac werefound during relapses (p<0.05). Results are expressed as ratios tobeta-actin (lower panel). (FIG. 5B) An example of a western blotrelevant to the expression of histone H3K9me2 (upper panel). Levels ofH3K9me2 in MS patients did not differ significantly from those incontrols. Results are expressed as ratios to beta-actin (lower panel).(FIG. 5C, FIG. 5D) Correlation of SIRT1 with histone H3K9ac and H3K9me2expression by Spearman's correlation coefficient. SIRT1 protein levelswere positively correlated with levels of H3K9ac (R=0.544, p=0.0196)(FIG. 5C) and H3K9me2 (R=0.716, p=0.0008) (FIG. 5D).

FIGS. 6A-6B. SIRT1 expression is mediated through RGC-32. PBMCs frompatients with stable MS were transfected with lentivirus RGC-32 shRNA orshCTR for 48 h. The expression of RGC-32 and SIRT1 mRNA was thendetermined using real-time PCR. (FIG. 6A) RGC-32 shRNA treatmenteffectively decreased mRNA RGC-32 expression by 78% when compared toshRNA control (shCTR)-transfected cells. (FIG. 6B) SIRT1 mRNA expressionwas reduced by 50% (p=0.01), indicating an important role for RGC-32 inmediating SIRT1 mRNA expression.

FIGS. 7A-7C. Effect of SIRT1 inhibition on annexin V binding. Jurkatcells (FIG. 7A) and CD4⁺ (FIG. 7B) and CD8⁺ (FIG. 7C) T cells from an MSpatient were pretreated with the SIRT1 inhibitor sirtinol (200 μM) for24 h, and Annexin V FITC binding was determined by FACS analysis.Overlay histograms are shown for untreated control cells (left peak ineach graph) and sirtinol treated cells (right peak in each graph). Asexpected, cells that were treated with the vehicle (DMSO) were primarilyAnnexin V negative. The small number of Annexin V negative cells incontrol cells represents the basal level of apoptosis. A significantincrease in Annexin V binding was found in all studied cells after 24 hof incubation with sirtinol for 24 h.

FIGS. 8A-8D. Effect of SIRT 1 inhibition on FasL expression. PBMCs froma stable MS patient (FIG. 8A, FIG. 8C) were pretreated with the SIRT1inhibitor sirtinol (200 μM) for 24 h (FIG. 8B, FIG. 8D), cultured withCD4⁺ (FIG. 8B) or CD8⁺ (FIG. 8D) T cells, and expression of FasL wasthen determined by FACS analysis. A significant increase in FasLexpression in both CD4⁺ (FIG. 8B) and CD8⁺ (FIG. 8D) T cells is seenafter treatment with the SIRT1 inhibitor.

FIG. 9. SIRT1 mRNA in responders and non-responders to GlatiramerAcetate (GA) treatment. SIRT1 mRNA expression was measured in patientPBMCs using real-time qRT-PCR and expressed as a ratio to L13.Significantly higher levels of SIRT1 mRNA were found in responders toglatiramer acetate (GA) compared to non-responders (p<0.01).

FIG. 10. Time course of SIRT1 mRNA expression in GA-treated MS patients.PBMCs were obtained from patients with RRMS at 0, 3, 6, and 12 monthsfollowing the initiation of GA treatment. SIRT1 mRNA expression wasmeasured in patient PBMCs using real-time qRT-PCR and expressed as aratio to L13. Responders to GA showed persistently higher levels ofSIRT1 mRNA compared to non-responders over time.

FIGS. 11A-11B. Receiver operating characteristic (ROC) curve analysis toassess the predictive accuracy of SIRT1 mRNA in detecting relapse andresponse to GA therapy. The probability (C-statistic, or area under thecurve (AUC)) of accurately detecting relapse was 72% (p<0.02), forresponse to GA therapy was 70% (p=0.04). (FIG. 11A) In the presentcohort, a SIRT1/L13 ratio<3.06 detected patient relapse with specificityof 81%. (FIG. 11B) A SIRT1/L13 ratio>4.33 detected patient response toGA therapy with a specificity of 73%. AUC, represented as a percentage,with a perfect score being 100% predictability.

FIG. 12. ROC curve analysis to assess the predictive accuracy of SIRT1protein in detecting relapse. The probability (C-statistic, or AUC) ofaccurately detecting relapse was 88% (p<0.047). In the present cohort, aSIRT1/L13 ratio<0.645 detected patient relapse with specificity of 80%.AUC, represented as a percentage, with a perfect score being 100%predictability.

FIGS. 13A-13F. Expression of RGC-32, FasL, CDC2, AKT, and IL-21 mRNA instable MS patients and patients with acute relapses. Target gene mRNAexpression was measured in patient PBMCs using real-time qRT-PCR andexpressed as a ratio to L13. (FIG. 13A) Significantly lower levels ofRGC-32 mRNA were found in patients with relapses compared to clinicallystable patients (p<0.0001). (FIG. 13B) Significantly lower levels ofFasL mRNA were found in patients with relapses compared to clinicallystable patients (p<0.0001). (FIG. 13C; FIG. 13D) No statisticallysignificant changes were observed in CDC2 or AKT mRNA. (FIG. 13E)Significantly higher levels of IL-21 mRNA were found in patients withrelapses compared to clinically stable patients (p=0.04). (FIG. 13)RGC-32 mRNA expression levels were correlated with those of FasL inpatients during relapses (r=0.90, p b 0.0001).

FIG. 14A-14E. Expression of RGC-32, FasL, CDC2, AKT, and IL-21 mRNA inresponders and non-responders to GA treatment. Target gene mRNAexpression was measured in patient PBMCs using real-time qRT-PCR andexpressed as a ratio to L13. (FIG. 14A) Significantly higher levels ofRGC-32 mRNA were found in responders to GA compared to non-responders(p<0.0001). (FIG. 14B) Significantly higher levels of FasL mRNA werefound in responders to GA compared to non-responders (p<0.0001). (FIG.14C; FIG. 14D) Levels of CDC2 and AKT mRNA were not significantlydifferent between responders to GA and non-responders. (FIG. 14E)Significantly decreased levels of IL-21 mRNA were found in responders toGA compared to non-responders (p=0.02).

FIGS. 15A-15C. Time course of RGC-32, FasL, and IL-21mRNA expression inGA-treated MS patients. PBMCs were obtained from patients with RRMS at0, 3, 6, and 12 months following the initiation of GA treatment. Targetgene mRNA expression was measured in patient PBMCs using real-timeqRT-PCR and expressed as a ratio to L13. (FIG. 15A) Responders to GAshowed persistently higher levels of RGC-32 compared to non-respondersover time. (FIG. 15B) A similar pattern was observed for FasL mRNAexpression, with higher levels of mRNA expression seen in responders andlower levels in non-responders over time. (FIG. 15C) Responders to GAshowed persistently lower levels of IL-21 compared to non-respondersover time.

FIGS. 16A-16B. Correlation of RGC-32 and FasL mRNA in GA-treated MSpatients. RGC-32 mRNA levels were correlated with those of FasL in bothresponders (FIG. 16A) and non-responders during relapses (FIG. 16B). ThePearson correlation coefficient for responders was r=0.53 (p=0.0003),and r=0.74 (p=0.01) for non-responders.

FIGS. 17A-17C. ROC curve analysis to assess the predictive accuracy ofRGC-32, FasL, and IL-21 mRNA in detecting MS patient relapse. Theprobability (C-statistic, or AUC) of accurately detecting relapse was90% using RGC-32 (p<0.0001), 88% using FasL (p<0.0001), and 75% usingIL-21 (p=0.01). (FIG. 17A) In the present cohort, a RGC-32/L13ratio<1.27 detected patient relapse with a sensitivity of 71% and aspecificity of 95%. (FIG. 17B) A FasL/L13 ratio<52.6 detected patientrelapse with a sensitivity of 81% and a specificity of 95%. (FIG. 17C)An IL-21/L13 ratio>16.9 detected patient relapse with a sensitivity of54% and a specificity of 88%.

FIGS. 18A-18C. ROC curve analysis to assess the predictive accuracy ofRGC-32, FasL, and IL-21 mRNA in detecting MS patient response to GA. Theprobability (C-statistic, or AUC) of accurately detecting response to GAtreatment over 2 years was 85% using RGC-32 (p=0.0002), 90% using FasL(p<0.0001), and 85% using IL-21 (p=0.001). (FIG. 18A) In the presentcohort, a RGC-32/L13 ratio>2.52 detected RRMS patient response to GAwith a sensitivity of 71% and a specificity of 92%. (FIG. 18B) AFasL/L13 ratio>85.4 detected RRMS patient response to GA with asensitivity of 85% and a specificity of 92%. (FIG. 18C) An IL-21/L13ratio<11.9 detected RRMS patient response to GA with a sensitivity of81% and a specificity of 89%.

FIG. 19. ROC curve analysis to assess the predictive accuracy of RGC-32,FasL, and SIRT1 mRNA in detecting MS relapse. The probability(C-statistic, or AUC) of accurately detecting relapse was 90% usingRGC-32 (p<0.0001), 88% using FasL (p<0.0001), and 72% using SIRT1(p=0.02).

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

Unless otherwise noted, technical terms are used according toconventional usage. Definitions of common terms in molecular biology maybe found, for example, in Benjamin Lewin, Genes VII, published by OxfordUniversity Press, 2000 (ISBN 019879276X); Kendrew et al. (eds.); TheEncyclopedia of Molecular Biology, published by Blackwell Publishers,1994 (ISBN 0632021829); and Robert A. Meyers (ed.), Molecular Biologyand Biotechnology: a Comprehensive Desk Reference, published by Wiley,John & Sons, Inc., 1995 (ISBN 0471186341); and other similar technicalreferences.

As used herein, “a” or “an” may mean one or more. As used herein whenused in conjunction with the word “comprising,” the words “a” or “an”may mean one or more than one. As used herein “another” may mean atleast a second or more. Furthermore, unless otherwise required bycontext, singular terms include pluralities and plural terms include thesingular.

As used herein, “about” refers to a numeric value, including, forexample, whole numbers, fractions, and percentages, whether or notexplicitly indicated. The term “about” generally refers to a range ofnumerical values (e.g., +/−5-10% of the recited value) that one ofordinary skill in the art would consider equivalent to the recited value(e.g., having the same function or result). In some instances, the term“about” may include numerical values that are rounded to the nearestsignificant figure.

II. The Present Invention

As briefly summarized above, the present inventors have found that thelevels of the biomarkers SIRT1, RGC-32, FasL and IL-21 vary in a subjecthaving RRMS based on the whether the subject is experiencing a relapse.Among other observations, the inventors found SIRT1 levels weresignificantly reduced in MS patients with relapses as compared tocontrol patients. In particular, decreased expression of SIRT1 was foundin PBMCs during relapse, thus demonstrating the protein may be used as amarker of disease activity. These observations form the basis of thepresent invention which is generally directed to methods for determiningwhether a subject previously diagnosed as having MS is undergoing arelapse of the disease and to predicting whether a subject having RRMSwill respond to treatment with glatiramer acetate (GA) based onexpression levels of the biomarkers SIRT1, RGC-32, FasL and IL-21.

Sirtuin 1 (SIRT1) is a member of the HDAC (histone deacetylase) classIII family of proteins (Smith et al., 2000). It is an NADtdependenthistone and protein deacetylase (Penberthy and Tsunoda, 2009; Smith etal., 2000) that catalyzes the removal of acetyl groups from a variety ofprotein substrates (Turner, 1998), including histones H1, H3, and H4(Turner, 1998; Wang et al., 2011; Zhang and Kraus, 2010). In addition,SIRT1 has been found to promote histone H3K9 methylation, resulting inepigenetic gene silencing (Imai et al., 2000; Vaquero et al., 2007;Vaquero et al., 2004). SIRT1 is involved in the regulation of a numberof cellular processes, including transcription, metabolism (Chen et al.,2008; He et al., 2012), DNA repair, and aging (Guarente, 2011). SIRT1can induce chromatin silencing through the deacetylation of histones(Baur, 2010) and can modulate cell survival by regulating thetranscriptional activities of p53 (Luo et al., 2000), NF-κB (Yeung etal., 2004), FOXO proteins (Brunet et al., 2004; Motta et al., 2004), andp300 (Bouras et al., 2005).

An association between SIRT1 and MS was suggested by the work ofShindler et al. (2010) who demonstrated resveratrol, a natural plantcompound currently being investigated for use in the treatment ofdiseases including cancer, was neuroprotective in MS patients. Furtherwork by Nimmagadda et al. (2013) showed the mechanism for theimmunomodulatory and neuroprotective effects of resveratrol involved theactivation of SIRT1.

Because little was known about the changes that occur in SIRT1expression or in the acetylation and methylation of histones in the PBMCand T cells from MS patients, the investigations reported herein whereundertaken. The observations provided herein elucidated the relationshipbetween SIRT1 and RRMS in subjects afflicted with the disease, and formthe basis of the invention. Based on the nexus between SIRT1 expressionand RRMS, the additional studies on other biomarkers were carried out,leading to the further discovery of a relationship between levels ofexpression of RGC-32, FasL and IL-21 and RRMS. The present inventionprovides methods for determining the status of relapse in subjectshaving RRMS and to predicting whether a subject having RRMS will respondto treatment using the drug glatiramer acetate (GA).

In a first embodiment, the invention is thus generally drawn to methodsfor determining whether a subject having relapsing-remitting multiplesclerosis (RRMS) is undergoing relapse of the disease by monitoringlevels of mRNA expression of certain biomarkers. In particular, theinvention is drawn to methods for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising

(i) determining mRNA expression levels for one or more biomarkersselected from the group consisting of SIRT1, RGC-32, FasL and IL-21 in apopulation of cells,

(ii) determining mRNA expression levels for L13 in the same populationof cells, and

(iii) calculating a ratio of biomarker mRNA expression to L13 mRNAexpression,

wherein when the biomarker is SIRT1 and the SIRT1/L13 ratio is<3.06±10%, the subject is determined to be undergoing relapse,wherein when the biomarker is RGC-32 and the RGC-32/L13 ratio is<1.27±10%, the subject is determined to be undergoing relapse,wherein when the biomarker is FasL and the FasL/L13 ratio is <52.6±10%,the subject is determined to be undergoing relapse, andwherein when the biomarker is IL-21 and the IL-21/L13 ratiois >16.9±10%, the subject is determined to be undergoing relapse.

In this embodiment, the range encompassing the noted SIRT1/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the SIRT1/L13 ratio is about <3.01, <3.02, <3.03,<3.04, <3.05, <3.06, <3.07, <3.08, <3.09, <3.10, <3.11, or <3.12.

In this embodiment, the range encompassing the noted RGC-32/L13 ratiocan also be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. Incertain preferred aspects, the RGC-32/L13 ratio is about <1.22, <1.23,<1.24, <1.25, <1.26, <1.27, <1.28, <1.29, <1.30, <1.31, <1.32, or <1.33.

In this embodiment, the range encompassing the noted FasL/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the FasL/L13 ratio is about <52.55, <52.56, <52.57,<52.58, <52.59, <52.6, <52.61, <52.62, <52.63, <52.64, <52.65 or <52.66.

In this embodiment, the range encompassing the noted IL-21/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the IL-21/L13 ratio isabout >16.85, >16.86, >16.87, >16.88, >16.89, >16.9, >16.91, >16.92, >16.93, >16.94, >16.95,or >16.96.

In the various aspects of this embodiment, mRNA expression levels forone, two, three or all of the four biomarkers is determined.

As indicated by this embodiment of the invention, the data obtained fromthe method will indicate whether the subject is undergoing relapse.Based on this information, a physician can determine the best course ofnew or continuing treatment for the subject. Thus, when the methodindicates that the subject is undergoing relapse, the method can furthercomprise administering a therapeutically effective amount of a treatmentfor RRMS to the subject. The treatment may be, for example, glatirameracetate (GA). Other suitable treatments for RRMS include, but are notlimited to, beta-interferons, teriflunomide, fingolimod, dimethylfumarate, and natalizumab.

In a second embodiment, the invention is generally drawn to methods fordetermining whether a subject having relapsing-remitting multiplesclerosis (RRMS) is undergoing relapse of the disease by monitoringlevels of protein expression of certain biomarkers. In particular, theinvention is drawn to methods for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising

(i) determining protein expression levels for SIRT1 in a population ofcells,

(ii) determining protein expression levels for L13 in the samepopulation of cells, and

(iii) calculating a ratio of SIRT1 protein expression to L13 proteinexpression,

wherein when the SIRT1/L13 ratio is <0.645±10%, the subject isdetermined to be undergoing relapse.

In this embodiment, the range encompassing the noted SIRT1/L13 ratio canalso be about ±4%, ±3%, ±2%, or ±1%. In certain preferred aspects, theSIRT1/L13 ratio is about <0.61, <0.62, <0.63, <0.64, <0.645, <0.65,<0.66, <0.67, <0.68, <0.69, or <0.70.

As indicated by this embodiment of the invention, the data obtained fromthe method will indicate whether the subject is undergoing relapse.Based on this information, a physician can determine the best course ofnew or continuing treatment for the subject. Thus, when the methodindicates that the subject is undergoing relapse, the method can furthercomprise administering a therapeutically effective amount of a treatmentfor RRMS to the subject. The treatment may be, for example, glatirameracetate (GA). Other suitable treatments for RRMS include, but are notlimited to, beta-interferons, teriflunomide, fingolimod, dimethylfumarate, and natalizumab.

In a third embodiment, the invention is generally drawn to methods fordetermining whether a subject having relapsing-remitting multiplesclerosis (RRMS) will respond to treatment with glatiramer acetate (GA).In particular, the invention is drawn to methods for determining whethera subject having relapsing-remitting multiple sclerosis (RRMS) willrespond to treatment with GA, comprising

(i) determining mRNA expression levels for one or more biomarkersselected from the group consisting of SIRT1, RGC-32, FasL and IL-21 in apopulation of cells,

(ii) determining mRNA expression levels for L13 in the same populationof cells, and

(iii) calculating a ratio of biomarker mRNA expression to L13 mRNAexpression,

wherein when the biomarker is SIRT1 and the SIRT1/L13 ratiois >4.33±10%, it is determined that the subject will respond totreatment with GA,wherein when the biomarker is RGC-32 and the RGC-32/L13 ratiois >2.52±10%, it is determined that the subject will respond totreatment with GA,wherein when the biomarker is FasL and the FasL/L13 ratio is >85.4±10%,it is determined that the subject will respond to treatment with GA, andwherein when the biomarker is IL-21 and the IL-21/L13 ratio is<11.9±10%, it is determined that the subject will respond to treatmentwith GA.

In this embodiment, the range encompassing the noted SIRT1/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the SIRT1/L13 ratio isabout >4.33, >4.27, >4.28, >4.29, >4.3, >4.31, >4.32, >4.33, >4.34, >4.35, >4.36, >4.37,or >4.38.

In this embodiment, the range encompassing the noted RGC-32/L13 ratiocan also be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. Incertain preferred aspects, the RGC-32/L13 ratio isabout >2.47, >2.48, >2.49, >2.50, >2.51, >2.52, >2.53, >2.54, >2.55, >2.56, >2.57,or >2.58.

In this embodiment, the range encompassing the noted FasL/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the FasL/L13 ratio isabout >85.35, >85.36, >85.37, >85.38, >85.39, >85.4, >85.41, >85.42, >85.43, >85.44, >85.45,or >85.46.

In this embodiment, the range encompassing the noted IL-21/L13 ratio canalso be about ±9%, ±8%, ±7%, ±6%, ±5%, ±4%, ±3%, ±2%, or ±1%. In certainpreferred aspects, the IL-21/L13 ratio is about <11.85, <11.86, <11.87,<11.88, <11.89, <11.9, <11.91, <11.92, <11.93, <11.94, <11.95, or<11.96.

In the various aspects of this embodiment, mRNA expression levels forone, two, three or all of the four biomarkers is determined.

As indicated by this embodiment of the invention, the data obtained fromthe method will indicate whether a subject having relapsing-remittingmultiple sclerosis (RRMS) will respond to treatment with glatirameracetate GA. Based on this information, a physician can determine thebest course of new or continuing treatment for the subject. Thus, whenit is determined that the subject will respond to treatment with GA, themethod further comprises administering a therapeutically effectiveamount of GA to the subject. When it is determined that the subject willnot respond to treatment with GA, the method further comprisesadministering a therapeutically effective amount of another, non-GAtreatment suitable for RRMS including, but not limited to,beta-interferons, teriflunomide, fingolimod, dimethyl fumarate, andnatalizumab.

In each of the embodiments and aspects of the invention, the populationof cells may be, but is not limited to, peripheral blood mononuclearcells (PBMCs), CD4+ T cells, CD8+ T cells, MAB328+ cells, GFAP+ cells,leukocytes, monocytes, glial cells, dendritic cells, and neurons.

In each of the embodiments and aspects of the invention, the methods mayinclude one or more of the following steps: (i) obtaining a biologicalsample from the subject, such as a sample of cells or a blood sample,(ii) isolating a selected cell type from a biological sample from thesubject, (iii) isolating polynucleotides from a selected cell type froma biological sample from the subject, (iv) isolating polypeptides from aselected cell type from a biological sample from the subject, (v)amplifying mRNA from isolated polynucleotides from a selected cell typefrom a biological sample from the subject, (vi) preparing cDNA fromisolated polynucleotides from a selected cell type from a biologicalsample from the subject, (vii) determining the level of mRNA expressionfor a selected biomarker in a selected cell type from a biologicalsample from the subject, (viii) determining the level of cDNA expressionfor a selected biomarker in a selected cell type from a biologicalsample from the subject, (ix) determining the level of proteinexpression for a selected biomarker in a selected cell type from abiological sample from the subject, (x) amplifying L13 mRNA fromisolated polynucleotides from a selected cell type from a biologicalsample from the subject, (xi) amplifying L13 cDNA from isolatedpolynucleotides from a selected cell type from a biological sample fromthe subject, (xii) determining the level of L13 mRNA expression in aselected cell type from a biological sample from the subject, (xiii)determining the level of L13 cDNA expression in a selected cell typefrom a biological sample from the subject, and (xiv) determining thelevel of L13 protein expression in a selected cell type from abiological sample from the subject.

In each of the embodiments and aspects of the invention, the subject isa human, a non-human primate, bird, horse, cow, goat, sheep, a companionanimal, such as a dog, cat or rodent, or other mammal.

III. Examples Materials and Methods Brain Tissue

Frozen brain tissue specimens acquired at autopsy from six patients witha definitive diagnosis of MS were obtained from the Human Brain andSpinal Fluid Resource Center, Veterans Affairs West Los Angeles HealthCare Center. Active lesions contained abundant infiltrates consisting ofT cells and macrophages, with detectable myelin degradation products.Inflammation was restricted to the lesion margins in chronic activelesions. Regions of normal-appearing white matter (NAWM) andnormal-appearing gray matter lesions (NAGM) that lacked macroscopic orhistological evidence of demyelination were also used. The samples werederived from patients between the ages of 38 and 51, with a mean age of47. Four healthy control brain samples from patients between the ages of36-72, with a mean age of 49, were obtained from the Cooperative HumanTissue Network, Charlottesville, Va.

Immunohistochemical Staining for SIRT1 and HDAC3

Immunohistochemical staining of brains from MS patients was performed aspreviously described (Cudrici et al., 2007). The air-dried cryostatbrain sections (4-6 μm) were fixed for 10 min in acetone containing 0.3%H₂O₂ to remove endogenous peroxidase. Tissue sections were blocked for10 min with 2.5% horse serum, then incubated overnight at 4° C. withrabbit anti-SIRT1 (Cell Signaling, Danvers, Mass.) or mouse monoclonalanti-SIRT1 (Active Motif, Carlsbad) as previously described (Fosbrink etal., 2005). For HDAC3 immunolocalization, a mouse monoclonal anti-HDAC3(BD Biosciences, San Jose, Calif.) was used. For phosphor-SIRT1, anantibody targeting serine 47(Cell Signaling) was used and forphosphor-HDAC3, an antibody targeting serine 424 (Assay Biotech,Sunnivale, Calif.) was used. The slides were washed three times for 3min each with PBS, pH 7.4, and then incubated with biotinylatedpan-specific universal antibody (Vector Labs, Burlingame, Calif.),followed by streptavidin/peroxidase complex reagent (Vector Labs).Specific reactions were developed using NovaRED (Vector Labs) as thesubstrate; slides were then counterstained with Harris's hematoxylin(Sigma, St. Louis, Mo.) and mounted with permanent mount. For CD4 andCD68 detection, brain cryosections were processed as described above andthen incubated with mouse monoclonal anti-CD4 antibody (NovoCastra,Newcastle upon Tyne, U.K.), diluted 1/50, for 2 h at room temperature(RT) or with mouse monoclonal CD68 (Dako, Carpenteria, Calif.), diluted1/200, for 1 h at RT. The sections were washed with PBS, pH 7.4, andthen incubated for 1 h at RT with HRP-conjugated goat anti-mouse IgG(Jackson Immunoresearch, West Grove, Pa.). Specific reactions were againdeveloped using NovaRED. The immunostained samples were analyzed by twoindependent scientists.

Double-Staining Immunohistochemistry

Frozen sections of brains from patients with MS were double-stained forSIRT1 and CD3, CD4, CD68, MAB328, or GFAP as previously described (Teglaet al., 2013). Cryosections were initially processed for SIRT1immunostaining as described above, and the reactions developed withNovaRED. Then slides were incubated with anti-CD4 mouse monoclonalantibody (NovaCastra), diluted 1/50 or with mouse monoclonal antibodyanti-CD68 (Dako) was followed by alkaline phosphatase-conjugated goatanti-mouse (Sigma), diluted 1/400. The reaction was developed using aVector alkaline phosphatase substrate kit III (Vector Labs). Similarreactions were performed for oligodendrocytes using a monoclonalantibody against oligodendrocytes/myelin (MAB328, Chemicon, Temecula,Calif.). For the double staining GFAP/SIRT1 the sections were firstincubated with mouse monoclonal anti-GFAP (Dako), diluted 1/1000 ON at4° C. The slides were washed several times in PBS and reacted with goatanti-mouse antibody (Santa Cruz Biotech) for 1 h at RT. The slides werethen exposed to NovaRED then exposed to the rabbit IgG anti-SIRT1followed by alkaline phosphatase conjugated anti-rabbit IgG (VectorLabs). The reaction was developed using a Vector alkaline phosphatasesubstrate kit III (Vector Labs). Control sections were prepared byimmunostaining without the primary antibody or by using control isotypeIgG instead of the primary antibody. The immunostained slides wereindependently evaluated by two investigators.

MS Patients and Controls

29 patients with relapsing-remitting MS (15 patients with stable diseaseand 14 with relapses) were enrolled in the study. The criteria forinclusion of MS patients in the study were: (i) age 18 to 65 years; (ii)fulfillment of McDonald criteria for definite MS (McDonald et al., 2001;Polman et al., 2005); (iii) relapsing-remitting course; (iv) havingnewly diagnosed MS, or MS not treated with currently usedimmunomodulatory drugs (interferon-β or glatiramer acetate) for 3 monthsprior to study entry; (v) no exacerbations in the 4 weeks before thestudy; (vi) no i.v. or p.o. steroids for 4 weeks prior to studyenrollment; (vii) no treatment with Tysabri, Gilenya, Tecfidera,mitoxantrone, cyclophosphamide, or investigational drugs during the pastyear; and (viii) a disability score of 0-5.5, as defined by the expandeddisability status scale (EDSS) (Kurtzke, 1983). Exclusion criteria forMS patients were: (i) a history of autoimmune disorders, vasculardisease, or active acute or chronic infections; (ii) use of antibioticsin the last 30 days; (iii) a history of intracranial or intraspinaltumor or metabolic myelopathy; or (iv) a history of alcohol or drugabuse. Fifteen healthy, age-, gender-, and race-matched healthy controlswere also enrolled in the study. Exclusion criteria for controls were:the presence of (i) overt acute or chronic disease(s) or (ii) otherautoimmune disease(s).

Collection of PBMCs, Total RNA Purification, and cDNA Synthesis

PBMCs were collected using BD Vacutainer CPT tubes (Becton Dickinson,Franklin Lakes, N.J.). The mononuclear cells were isolated from freshblood as previously described (Tegla et al., 2013). RNA isolation andcell lysate preparation for protein analysis were performed the same day(Niculescu et al., 1997). Total RNA was purified using the RNeasy MiniKit (Qiagen, Santa Clarita, Calif.) according to the manufacturer'sinstructions. RNA (0.5 μg per sample) was mixed with RT buffer, dNTP,and oligo-dT primer (Invitrogen). RNA was denatured by incubation at 65°C. for 5 min. The reverse transcriptase (Promega) and RNase inhibitor(Invitrogen) were then added, and the reaction mixture was incubated at37° C. for 1 h. The reaction was terminated by incubating the mixture at95° C. for 5 min (Tegla et al., 2013).

Real-Time PCR

Real-time PCR was performed using a StepOne real-time PCR system(Applied Biosystems, Foster City, Calif.). The primers for the genesinvestigated were designed and synthesized by IDT (Coralville, Iowa)(Table 1) and used in conjunction with LightCycler FastStart SYBR GreenMaster (Roche) according to the manufacturer's protocol.

TABLE 1 Primers used for Real-Time PCR Gene SEQ Product SymbolPrimer Sequence ID NO: (bp) SIRT1 For: 5′-TGGCAAAGGA  1 159GCAGATTAGTAG-3′ Rev: 5′-GGCATGTCCC  2 ACTATCACTGT-3′ HDAC3For: 5′-CATGCACCTA  3 182 GTGTCCAGATTC-3′ Rev: 5′-CACTCTTAAA  4TCTCCACATCGC-3′ RGC-32 For: 5′-AGGAACAGCT  5 152 TCAGCTTCAG-3′Rev: 5′-GCTAAAGTTT  6 TGTCAAGATCAGCA-3′ FasL For: 5′-GCCCATTTAA  7 110CAGGCAAGTC-3′ Rev: 5′-ATCACAAGGC  8 CACCCTTCTT-3′ L13 For: 5′-CGTGCGTCTG 9 227 AAGCCTACA-3′ Rev: 5′-GGAGTCCGTG 10 GGTCTTGAG-3′ CDC2For: 5′-TTTTCAGAGC 11 100 TTTGGGCACT-3′ Rev.: 5′-AGGCTTCCT 12GGTTTCCATTT-3′ AKT1 For: 5′-ACGCCAAGGA 13 185 GATCATGC-3′Rev.: 5′-CTCCATGCT 14 GTCATCTTGGTC-3′ Abbreviations: For, forwardprimer; Rev, reverse primer; Bpp, base pairs; RGC-32, response gene tocomplement 32; FasL, Fas ligand; SIRT1, Sirtuin 1; HDAC3, HistoneDeacetylase 3; L13, ribosomal protein L13.

As a negative control for each real-time PCR assay, the same reactionwas performed in the absence of cDNA or reverse transcriptase. For eachgene, the cycle threshold (C_(T)) values were determined in theexponential phase of the amplification plot and normalized bysubtraction of the C_(T) value for 18S (generating a ΔC_(T) value). Theresults were normalized to L13 ribosomal protein, a housekeeping gene. Astandard curve was generated using serial dilutions of qPCR ReferenceTotal cDNA (Clontech, Mountain View, Calif.), and the normalized mRNAvalue (NRV) was calculated according to the following formula forrelative expression of target mRNA: NRV (TarS/L13), where TarSrepresents the level of mRNA expression of the target gene, and L13corresponds to that of the amplified L13 mRNA. In some cases, the -foldchange in target gene samples, after normalization with the housekeepinggene (18S), was calculated using the 2^(−ΔΔCT) value, whereΔΔC_(T)=ΔC_(T) (sample)−ΔC_(T) (control) and ΔCT is the C_(T) value oftarget gene normalized to the C_(T) value of the housekeeping gene(Tegla et al., 2013).

RGC-32 Silencing and Transfection of Cells

Transfection of PBMCs:

PBMCs were plated in RPMI-10% FBS in 12-well plates 24 h prior to viralinfection. After 24 h, the medium from the plate wells was removed andreplaced with 1 ml of polybrene/RPMI-10% FBS medium mixture per well.Cells were then infected by adding the RGC-32 shRNA lentiviral particles(Santa Cruz Biotech) or control lentiviral particles (Santa CruzBiotech) to the culture medium overnight, as previously described (Teglaet al., 2013). The next day, the culture medium was removed and replacedwith 1 ml of RPMI-FCS 10%, and after 24 h, the transfected cells wereanalyzed for the expression of RGC-32, SIRT1, and L13 mRNA by real-timePCR as described above.

Annexin V Assay:

PBMCs and Jurkat cells were plated in RPMI-10% FBS in 12-well plates 24h prior to Annexin V FITC FACS analysis. Some of the cells were treatedwith sirtinol (200 μM) and the binding of Annexin V-FITC to cells wascompared with that of cells exposed to vehicle (DMSO) only. Annexin Vassay was performed according to manufacturer instructions (BDBiosciences) and only Annexin V FITC positive, propidium iodide negativecells were used in the evaluations since they are reflecting earlyapoptosis.

Western Blotting

Western blotting was performed as previously described (Rus et al.,1996a; Rus et al., 1996b). PBMC were washed with PBS, then lysed in abuffer consisting of 10 mM Tris-HCl (pH 7.4), 1 mM EDTA, 1 mM EGTA, 1 mMNaF, 20 mM Na₄P₂O₇, 1% Triton X-100, 0.1% SDS, 100 mM NaCl, 10%glycerol, 0.5% sodium deoxycholate, 1 mM Na₃VO₄, and complete miniprotease inhibitor mixture (Roche Applied Science, Indianapolis, Ind.),which was added just prior to use. Protein concentrations weredetermined using a BCA protein assay kit (Pierce, Rockford, Ill.).Lysates (30 μg of protein) were fractionated on 10% gradientSDS-polyacrylamide gels and transferred to nitrocellulose membranes(Millipore, Bedford, Mass.). The following primary antibodies were used:rabbit IgG anti H3K9ac (Cell Signaling, Danvers Mass.) and mousemonoclonal anti-SIRT1 and rabbit IgG anti-H3K9me2 (both from ActiveMotif Carlsbad, Calif.). Goat anti-rabbit or goat anti-mouse IgGHRP-conjugated Ab (Santa Cruz Biotech., Santa Cruz, Calif.), asappropriate, was used as a secondary antibody. For detection, enhancedchemiluminescence (ECL, Pierce) was used. Membranes were stripped usingRestore Western Blot Stripping Buffer (Pierce) and reprobed for theexpression of (3-actin (Rockland Immunochemicals, Rockville, Md.). Theradiographic band density was measured using UN-SCAN-IT software (SilkScientific, Orem, Utah) and results expressed as ratio to (3-actin.

Patients Treated with Glatiramer Acetate (GA)

A total of 15 patients with RRMS were enrolled in the study. Thepatients were recruited from the University of Maryland MultipleSclerosis Center. The mean age was 40 (range, 22-60), and consisted of60% females (n=9) and 40% males (n=6). The criteria for inclusion of MSpatients in the study were: (i) age 18 to 65 years; (ii) fulfillment ofthe McDonald criteria for definite MS (McDonald et al., 2001; Polman etal., 2005); (iii) relapsing-remitting course; (iv) having newlydiagnosed MS, or MS not treated with currently used immunomodulatorydrugs (interferon-β or glatiramer acetate) for 3 months prior to studyentry; (v) no exacerbations in the 4 weeks before the study; (vi) noi.v. or p.o. steroids for 4 weeks prior to study enrollment; (vii) notreatment with Tysabri, Gilenya, mitoxantrone, cyclophosphamide, or anyinvestigational drug during the past year; and (viii) a disability scoreof 0-5.5, as defined by the expanded disability status scale (EDSS)(Kurtzke, 1983). Exclusion criteria for MS patients were: (i) a historyof autoimmune disorders, vascular disease, or active acute or chronicinfections; (ii) use of antibiotics in the last 30 days; (iii) a historyof intracranial or intraspinal tumor or metabolic myelopathy; or (iv) ahistory of alcohol or drug abuse.

All MS patients received 20 mg of glatiramer acetate (GA) injectedsubcutaneously every day for 2 years. During this period of 2 years,patients were clinically evaluated and peripheral blood samples werecollected at 0, 3, 6, and 12 months at the time of their outpatientvisits. Patients with symptoms suggestive of a clinical relapse calledthe University of Maryland Multiple Sclerosis Center. Clinical relapsewas defined as substantial worsening of pre-existing symptoms orappearance of new neurological deficits in the absence of fever orinfections lasting more than 24 h. An EDSS evaluation was completed ateach visit. Clinical records, consultation reports, and inpatientrecords were reviewed by a neurologist to ensure that the data obtainedwere complete. In the case of patients with relapse, the administrationof 1 g of Solu-Medrol i.v. for 3 days was used to treat the diseaseexacerbation. A prednisone taper was also used after i.v. Solu-Medrol incertain cases. In such cases, blood samples were obtained prior toSolu-Medrol treatment. Responders to GA treatment were defined aspatients who exhibited 0 or no more than 1 relapse event during the 2year span following the initiation of GA. Non-responders were defined aspatients who exhibited 2 or more relapse events during the 2 year spanfollowing the initiation of GA. According to these criteria, the presentcohort consisted of 11 responders (mean age 43, range 27-60; 55% female)and 4 non-responders (mean age 31, range 22-36; 75% female).

Statistical Analysis

Comparisons between multiple groups were performed using two-way ANOVAor a two-tailed t-test assuming unequal variances. P values <0.05 wereconsidered significant. Pearson correlation analysis was conducted toexamine the association between variables. Statistical analysis wasperformed using SAS software, version 9.2, or IBM SPSS Statisticssoftware version 22 and GraphPad Prism software version 6. All valuesare shown as means±SEM and are representative of three experimentsunless otherwise noted. Receiver operating characteristic (ROC) curveanalysis was used to assess the predictive accuracy of each potentialbiomarker. The predictive probability of binary outcomes regardingclinical state and response to GA treatment was reported as aC-statistic or Area Under the Curve (AUC, represented as a percentage,with a perfect score being 100% predictability).

Results Immunohistochemical Localization of SIRT1 and HDAC3 in MS Brain

Since effector T cells migrate into the brain at the time of an MSrelapse (Costantino et al., 2008; Martinez-Pasamar et al., 2013), theexpression of SIRT1 in MS brains was investigated in relation to that ofT cells and macrophages. First, the localization of SIRT1 in 20 areasfrom 8 patients with MS (Table 2) was examined.

MS brain samples from active lesions contained abundant inflammatorycell infiltrates, consisting of CD4⁺ and CD8⁺ T cells as wellmacrophages. Acute active lesions contained inflammatory cellsthroughout the entire lesion, whereas the inflammation was restricted tothe lesion margins in chronic active lesions (Cudrici et al., 2007). Itwas found that SIRT1 was expressed in both acute and chronic activelesions (FIGS. 1 and 2, Table 2). SIRT1 was also found to be present oncells in both perivascular (FIG. 1A, B) and parenchymal areas (FIG. 1C).The SIRT1 deposition was confined not only to MS plaques but was alsopresent in areas of NAWM and NAGM. In general, the expression of SIRT1was higher in the MS plaques than in NAWM and NAGM (Table 2).

TABLE 2 Expression of SIRT1, phospho-SIRT1, HDAC3 and phospho-HDAC3 inMS brain. Phospho- Phospho- SIRT1 SIRT1 HDAC3 HDAC3 Case no. Peri-Paren- Peri- Paren- Peri- Paren- Peri- Paren- (Age, sex) Lesion (no.)Lesion Type vascular chymal vascular chymal vascular chymal vascularchymal 1 Occipital (3) Chronic active ++ ++ +++ +++ +/++ + ++ ++ (53, F)NAWM ++ ++ +++ +++ +/++ ++ ++ ++ NAGM + ++ ++/+++ ++/+++ ++ +++ + ++Parietal (3) Chronic active ++ ++ ++/+++ +++ ++ +/++ ND ND NAWM ++ +++++/+++ ++/+++ +/++ +++ +/++ ++ NAGM ++ ++ +++ +++ + ++ +/++ ++ 2Parietal (3) Acute ++ +++ ND ND +/++ ++ ND ND (68, M) NAWM ++ +++ ++++++ +++ ++ ND ND NAGM +/++ ++ +++ +++ ++ ++ + +++/++ 3 Parietal (3)Acute ++ +++ ND ND ++ ++/+++ ++ ++ (62, M) NAWM +++ +++ ND ND + ++ ++ ++NAGM + ++ ND ND + ++ ++ +++ 4 Frontal (3) Chronic active + +/++ +++ +++ND ND ND ND (38, F) NAWM + ++ +++ +++ +/++ ++ ND ND NAGM + + +++ +++ + +ND ND 5 Frontal (2) Chronic active + ++ +++ ++/+++ + ++ + ++ (51, F)NAGM + +/++ ++ ++ ++ ++ ND ND 6 Parietal (3) Acute +/++ +++ +++ +++ + +ND ND (47, F) NAWM +/++ +++ +++ +++ + + ND ND NAGM ++ ++ +++ +++ +++ ++ND ND Abbreviations used in the table: F: female; M: male; NAWM: normalappearing white matter; NAGM: normal appearing gray matter; ND:non-determined; + slightly positive; ++ positive; +++ highly positive.

SIRT1 was not found to be expressed in normal brain, with the exceptionof rare neurons in the cortex. Controls for the immunoperoxidasereaction using isotype IgG instead of the primary antibody were allnegative (FIG. 1D). The expression of HDAC3 in MS brain was alsoinvestigated since this protein was previously reported to be expressedby PBMCs of MS patients (Zhang et al., 2011). Like SIRT1, HDAC3 was alsofound to be present in periventricular and parenchymal areas of MSbrains (FIG. 2A, B) (Table 2). The HDAC3 deposition was confined notonly to MS plaques but was also present in areas of NAWM and NAGM (Table2). Expression of HDAC3 was higher in the MS plaques than in NAWM andNAGM. Since both SIRT1 and HDAC3 are regulated by phosphorylation(Sasaki et al., 2008; Zhang et al., 2005), these phosphorylated proteinswere localized to MS brains. It was found that SIRT1 phosphorylated(p-SIRT1) at Ser 47 and HDAC3 phosphorylated (p-HDAC3) at Ser 424 werealso widely distributed in MS plaques as well as NAGM and NAWM (FIG. 1C,2C) (Table 2). P-SIRT1 deposits were found only in the nucleus (FIG.1C), whereas p-HDAC3 was found to be localized both in the cytoplasm andin the nucleus (FIG. 2C).

Co-Localization of SIRT1 with CD4-, CD68-, MAB328-, and GFAP-PositiveCells

To further concentrate efforts on investigating whether CD4- andCD68-positive cells also express SIRT1, double-labeling experiments werecarried out using specific antibodies. It was discovered that some ofthe SIRT1 deposits co-localized with CD4⁺ cells (FIG. 3A). It was alsofound that some of the CD68⁺ cells in MS plaques co-localized with SIRT1(FIG. 3B). In addition, SIRT1 was present on CD68⁺ cells that hadmorphology suggestive of glial cells (data not shown). In addition toCD4- and CD68-positive cells, MAB328 and GFAP-positive cells alsoco-localized with SIRT1 (FIG. 3C, D), indicating that OLG and astrocytesin MS brains also express SIRT1. Immunoperoxidase reaction controls byreplacing primary antibodies with PBS were negative (FIG. 3F).

Expression of SIRT1 and HDAC3 in PBMCs of RR MS Patients and Controls

The expression of SIRT1 and HDAC3 in unstimulated PBMCs was nextexamined in relation to disease activity. Expression of SIRT1, HDAC3,and L13 (a housekeeping gene) mRNA was measured by real-time PCR. MSsamples were divided into those from stable periods in which no clinicalactivity was present and those from periods of relapse in which clinicalactivity was present and had been detected by a neurologist. Astatistically significant decrease in SIRT1 mRNA was seen in patientswith relapses when compared to controls (p<0.04). Stablerelapsing-remitting MS patients had levels of SIRT1 mRNA expression thatwere similar to those of control subjects (FIG. 4A). Also, HDAC3 mRNAlevels were not significantly changed in MS patients when compared tocontrols (FIG. 4B). SIRT1 protein expression was determined by westernblotting, and levels of SIRT1 protein were also found to besignificantly decreased in patients with relapses when compared tostable MS patients (p<0.01) and controls (p<0.02) (FIG. 3C). All thesedata indicate a significant decrease in SIRT1 levels during relapses.

Expression Profile of Histone H3K9Ac and H3K9Me2 in MS Patients

Acetylation and methylation of histone H3 at lysine 9 were assessed bywestern blotting using specific antibodies. Statistically significanthigher levels of H3K9ac were found during relapses (p<0.05). A reductionin H3K9 me2 was observed in the PBMCs of stable MS patients whencompared to controls, but this difference was not statisticallysignificant. SIRT1 protein levels were positively correlated withexpression of H3K9me2 (R=0.716, p=0.0008) and of H3K9ac (R=0.544,p=0.0196) (FIG. 5). These changes are in agreement with the describedrole of SIRT1 in H3K9 acetylation, with increased acetylation aconsequence of the reduced levels of SIRT1 during relapses. SIRT1 is aknown regulator of H3K9 methylation and can induce both an increase inmethylation and gene silencing (Vaquero et al., 2007; Vaquero et al.,2004).

Effect of RGC-32 Silencing on SIRTI Expression

It was previously shown that SIRT1 expression is regulated by RGC-32 inthe SW480 tumor cell line (Vlaicu et al., 2010). To investigate whetherRGC-32 is also required for the expression of SIRT1 mRNA in PBMCs,shRNAs targeting RGC-32 was used to silence its expression. PBMCs weretransfected with RGC-32 shRNA lentivirus and then tested by realtime-PCR to verify their effectiveness in blocking the endogenousexpression of RGC-32 mRNA. It was confirmed that RGC-32 shRNAeffectively decreased mRNA RGC-32 expression (by 72%) when compared tocells transfected with control shRNA (shCTR) (FIG. 6A). The ability ofRGC-32 shRNA to block SIRT1 mRNA expression was then examined. As shownin FIG. 6B, SIRT1 expression was reduced by 50% after RGC-32 silencing,indicating an important role for RGC-32 in SIRT1 expression. These dataare in agreement with the reported low levels of RGC-32 in MS patientswith relapses (Tegla et al., 2013).

Effect of SIRTI Inhibition on Apoptosis and FasL Expression

The effect of sirtinol on apoptosis was investigated in the Jurkat cellline, CD4⁺, and CD8⁺ cells. It was found that sirtinol (200 μM) inducedbinding of Annexin V in 65% of the Jurkat cells (as compared to 6% ofthe control cells exposed to vehicle DMSO). Similarly, increasedapoptosis as seen when CD4 cells (6% in control cells vs 55% in the MSpatient) and CD8 cells (22% in control cells vs 81% in the MS patient)were exposed to sirtinol for 24 h (FIG. 7). In order to investigate theeffect of SIRT1 inhibition on FasL expression, PBMCs from stable MSpatients were used. It was found that sirtinol (200 μM) significantlyinhibited the expression of SIRT1 mRNA (by 50%, data not shown) andsignificantly increased FasL expression (FIG. 8), suggesting a role forSIRT1 in the expression of FasL.

Expression of SIRTI in Responders Vs Non-Responders

SIRT1 mRNA expression was measured in patients' PBMCs using real-timeqRT-PCR and expressed as a ratio to L13. Responders to GA treatment weredefined as patients who exhibited 0 or no more than 1 relapse eventduring the 2 year span following the initiation of GA whereasnon-responders exhibited 2 or more relapse events. Significantly higherlevels of SIRT1 mRNA were found in responders to GA compared tonon-responders (p<0.01) (FIG. 9). Next we examined the time course ofSIRT1 mRNA expression in GA-treated MS patients. PBMCs were obtainedfrom patients with RRMS at 0, 3, 6, and 12 months following theinitiation of GA treatment. SIRT1 mRNA expression was measured inpatients' PBMCs using real-time qRT-PCR and expressed as a ratio to L13.A. Responders to GA showed persistently higher levels of SIRT1 comparedto non-responders over time (FIG. 10).

ROC Analysis

ROC analysis was used to assess the predictive accuracy of using SIRT1mRNA level to detect patient relapse. The probability (C-statistic, orarea under the curve (AUC)) of accurately detecting relapse was 72%using SIRT1. In the present cohort, a SIRT1/L13 ratio<3.06 detectedpatient relapse with specificity of 81% (FIG. 11A).

ROC analysis was used to assess the predictive accuracy of using SIRT1mRNA level to detect response to GA. The probability (C-statistic, orarea under the curve (AUC)) of accurately detecting response to GA was70% (p=0.04). Using 1SIRT1/L13 ratio>4.33 detected patient response toGA therapy with a specificity of 73% (FIG. 11B).

ROC curve analysis was also used to assess the predictive accuracy ofSIRT1 protein in detecting relapse (FIG. 12). The probability(C-statistic, or AUC) of accurately detecting relapse was 88% using(p<0.047). In the present cohort, a SIRT1/L13 ratio<0.645 detectedpatient relapse with specificity of 80%.

Expression of RGC-32, FasL, CDC2, AKT, and IL-21 mRNA in Acute MSRelapse

The expression of RGC-32 mRNA in unstimulated PBMCs was examined inrelation to disease activity. FasL and CDC2 mRNA expression were alsoinvestigated because RGC-32 is known to bind to and regulate CDC2, whichin turn has a regulatory effect on FasL expression (Badea et al., 2002;Fosbrink et al., 2009; Torgler et al., 2004). In addition, IL-21 and AKTmRNA expression were investigated as previously described (Tegla et al.,2013). MS patient PBMC samples were categorized into those from stableperiods in which no clinical activity was present and those from periodsof relapse, in which clinical activity was present and had been detectedby a neurologist. Target gene mRNA expression was measured in patientPBMCs using real-time qRT-PCR and expressed as a ratio to L13.Statistically significant lower levels of RGC-32 mRNA were found in MSpatients with relapses compared to those who were clinically stable(p<0.0001) (FIG. 13A). Patients with relapses also exhibitedsignificantly lower levels of FasL mRNA compared to stable MS patients(p<0.0001) (FIG. 13B). Levels of CDC2 and AKT mRNA in MS patients withrelapses were similar to those in stable patients (FIG. 13C, D). On theother hand, IL-21 mRNA expression was significantly higher in MSpatients with relapses compared to stable MS patients (p=0.04) (FIG.13E). As shown in FIG. 13F, RGC-32 and FasL mRNA expression levels werepositively correlated within MS patients during relapses (r=0.90,p<0.0001).

Expression of RGC-32, FasL, CDC2, AKT, and IL-21 mRNA in Responders Vs.Non-Responders to GA Treatment

Since GA is an effective treatment for RRMS, the relationship betweenRGC-32, FasL, CDC2, AKT, and IL-21 mRNA expression and responsiveness totreatment over time was investigated. Responders to GA treatment weredefined as patients who exhibited 0 or no more than 1 relapse eventduring the 2 year span following the initiation of GA whereasnon-responders exhibited 2 or more relapse events. Overall, respondersto GA treatment showed significantly higher levels of RGC-32 (p<0.0001)and FasL (p<0.0001) (FIG. 14A, B). No significant change was observed inCDC2 or AKT expression between responders and non-responders (FIG. 14C,D). IL-21 mRNA levels were lower in responders to GA treatment comparedto non-responders (p=0.02) (FIG. 14E).

Over time, responders to GA showed persistently higher levels of RGC-32,whereas non-responders showed persistently lower levels (FIG. 15A). Asimilar pattern was observed for FasL (FIG. 15B), with higher levels ofmRNA expression seen in responders and lower levels seen innon-responders over time. Conversely, over time responders to GA showedpersistently lower levels of IL-21, whereas non-responders showedpersistently higher levels (FIG. 15C). CDC2 and AKT mRNA expression didnot exhibit a pattern that differed between responders andnon-responders over time (data not shown).

Furthermore, RGC-32 and FasL mRNA levels were positively correlatedwithin responders during periods of both remission and relapse, as wellas non-responders during relapse (FIG. 16A, B). Pearson correlationcoefficients were r=0.53 (p=0.0003) for responders and r=0.74 (p=0.01)for non-responders during relapse. No statistically significantcorrelations were found between EDSS scores and any of the target genesexamined (data not shown).

ROC Analysis

ROC analysis was used to assess the predictive accuracy of using mRNAlevels of each putative biomarker to detect patient relapse. Theprobability (C-statistic, or AUC) of accurately detecting relapse was90% using RGC-32 (95% CI 80-99%, p<0.0001), 88% using FasL (95% CI77-99%, p<0.0001), and 75% using IL-21 (95% CI 58-91%, p=0.01) (FIG.17). In the present cohort, a RGC-32/L13 ratio<1.27 detected patientrelapse with a sensitivity of 71% (95% CI 44-90%) and a specificity of95% (95% CI 82-99%) (FIG. 17A). A FasL/L13 ratio<52.6 detected patientrelapse with a sensitivity of 81% (95% CI 54-96%) and a specificity of95% (95% CI82-99%) (FIG. 17B). An IL-21/L13 ratio>16.9 detected patientrelapse with a sensitivity of 54% (95% CI 25-81%) and a specificity of88% (95% CI 72-97) (FIG. 17C).

Since persistently higher levels of RGC-32 and FasL as well as lowerlevels of IL-21 mRNA were associated with a good response to GAtreatment over time, ROC analysis was also used to assess the predictiveaccuracy of RGC-32, FasL, and IL-21 in detecting response to GA. Theprobability (C-statistic, or AUC) of accurately detecting response to GAtreatment over 2 years was 85% using RGC-32 (95% CI 74-95%, p=0.0002),90% using FasL (95% CI 81-100%, p<0.0001), and 85% using IL-21 (95% CI71-99%, p=0.001) (FIG. 18). In the present cohort, a RGC-32/L13ratio>2.52 correctly detected patient response to GA with a sensitivityof 71% (95% CI 54-84%) and a specificity of 92% (95% CI 64-100%). AFasL/L13 ratio>85.4 correctly detected patient response to GA with asensitivity of 85% (95% CI 71-94%) and a specificity of 92% (95% CI64-100%). An IL-21/L13 ratio<11.9 correctly detected patient response toGA with a sensitivity of 81% (95% CI 65-92%) and a specificity of 89%(95% CI 52-100%).

Additionally, ROC curve analysis was performed using only baseline mRNAlevels from samples collected prior to GA administration (i.e. at month0) to assess the predictive accuracy of initial RGC-32, FasL, and IL-21levels in predicting future response to GA. The probability(C-statistic, or AUC) of accurately predicting response to GA was 82%using RGC-32 (95% CI 58-100%, p=0.10), 100% using FasL (95% CI 100-100%,p=0.03), and 75% using IL-21 (95% CI 35-100%, p=0.28) (data not shown).

Additional ROC analysis data using four of the biomarkers (RGC-32, FasL,IL-21, SIRT1) is presented in Tables 3 and 4, and in FIG. 18. This dataindicates that these four biomarkers alone or in combination could serveas potential biomarkers to predict relapses and response to treatment.

TABLE 3 Receiver operating characteristic (ROC) curve analysis to assessthe predictive accuracy of RGC-32, FasL, IL-21, and SIRT1 mRNA indetecting MS patient relapse. RGC-32 FasL IL-21 SIRT1 Area Under 90% 88%75% 88% Curve (p < 0.0001) (p < 0.0001) (p = 0.001) (p < 0.047) Cut-Off<1.27 <52.6 >16.9 <3.06 (Ratio to L13) Sensitivity 71% 81% 54% 54%Specificity 95% 95% 88% 81% AUC, represented as a percentage, with aperfect score being 100% predictability. Cut-off was calculated as ratioof target gene to L13 (housekeeping gene).

TABLE 4 Receiver operating characteristic (ROC) curve analysis to assessthe predictive accuracy of RGC-32, FasL, IL-21, and SIRT1 mRNA indetecting MS patient response to GA. RGC-32 FasL IL-21 SIRT1 Area Under85% 90% 85% 88% Curve (p = 0.0002) (p < 0.0001) (p = 0.001) (p < 0.047)Cut-Off >2.52 >85.4 <11.9 <0.645 (Ratio to L13) Sensitivity 71% 85% 81%54% Specificity 92% 92% 89% 80% AUC, represented as a percentage, with aperfect score being 100% predictability. Cut-off was calculated as ratioof target gene to L13 (housekeeping gene).

DISCUSSION

The data provided herein reveals that inflammatory cells (T cells andmacrophages), OLG, and astrocytes all express SIRT1 in the MS brain. Theexpression of SIRT1 was not confined to the MS plaques but was alsopresent in NAWM and NAGM areas, indicating a widespread distribution ofcells expressing SIRT1.

To gain more insight into the role played by SIRT1 in inflammatorycells, the expression of SIRT1 mRNA in PBMCs was examined, in relationto disease activity in MS patients. This analysis was performed inunstimulated PBMCs in order to mimic the in vivo situation as closely aspossible (Lopatinskaya et al., 2003). The levels of SIRT1 were found tobe significantly decreased in the PBMCs of MS patients with relapseswhen compared to those of healthy controls. These data suggest that lowlevels of SIRT1 can be used a possible biomarker of disease activity inMS patients.

To further investigate the factors that might regulate SIRT1 expression,it was asked whether RGC-32 might be involved in SIRT1 expression. Itwas found that silencing of RGC-32 in PBMCs led to a significantdecrease in SIRT1 expression. These data suggest that the expression ofSIRT1 is regulated by RGC-32, and they confirm previous observations incancer cell lines (Vlaicu et al., 2013; Vlaicu et al., 2010). Thisfinding is important because RGC-32 was found to promote cell cycleactivation and survival through the activation of the cdc2/cyclinB1complex (Badea et al., 2002; Badea et al., 1998), which alsophosphorylates and activates SIRT1 (Sasaki et al., 2008). This datasuggest that regulation of SIRT1 expression is an additional mechanismby which RGC-32 promotes survival. It is also entirely possible that thelow levels of RGC-32 expression seen in the PBMCs of MS patients withrelapses are responsible for the reduction in SIRT1 expression seenduring the active phase of the disease.

To further investigate the relationship between SIRT1 and T-cellsurvival, the effect of the SIRT1 inhibitor sirtinol on apoptosis andFasL expression was examined. It was found that the expression of FasLwas significantly increased, indicating that FasL expression is, atleast in part, SIRT1-dependent. In addition, inhibition of SIRT1 leadsto significant apoptosis in Jurkat cells and in CD4⁺ and CD8⁺ frompatients with MS. These results showing a decreased level of SIRT1 in MSpatients with relapses are in agreement with recent data obtained inEAE, an animal model of MS. These experiments showed that administrationof resveratrol, a SIRT1 activator, ameliorates the disease course in EAE(Nimmagadda et al., 2013). In addition, resveratrol was found to triggerapoptosis in activated T cells and also to induce a decrease in spinalcord inflammation during EAE (Singh et al., 2007). Resveratrol was alsofound to be neuroprotective (Shindler et al., 2010), and the mechanismfor its immunomodulatory and neuroprotective effects appears to involvethe activation of SIRT1 (Singh et al., 2007).

ROC analysis showed that SIRT1 mRNA and protein levels accuratelydetected patient relapse and patient response to GA treatment.

In light of these initial studies, RGC-32, FasL, CDC2, AKT, and IL-21were evaluated as potential biomarkers of relapse and response to GAtreatment in a cohort of MS patients over time. This analysis was alsoperformed in unstimulated PBMCs in order to mimic the in vivo situationas closely as possible, so that alterations in mRNA expression wouldhave greater predictive value with respect to clinical exacerbations(Lopatinskaya et al., 2003).

It was previously shown that RGC-32 and FasL mRNA levels aresignificantly decreased and that IL-21 levels are increased in the PBMCsof MS patients during clinical relapse compared to remission (Tegla etal., 2013). The present data extend and confirm these prior results in agreater number of patients. Furthermore, ROC analysis of this cohortshowed that RGC-32, FasL, and IL-21 mRNA levels accurately detectedpatient relapse (FIG. 17). Together, these findings support the use ofRGC-32, FasL, and IL-21 as potential serum biomarkers of diseaseactivity in multiple sclerosis.

Overall, RGC-32 and FasL mRNA levels were significantly increased andIL-21 levels were decreased in the PBMCs of MS patients defined asresponders compared to non-responders to GA. Over time, RGC-32 and FasLlevels were persistently higher and IL-21 levels were persistently lowerin responders versus non-responders as well. Furthermore, ROC analysisof this cohort showed that RGC-32, FasL, and IL-21 mRNA levelsaccurately detected patient response to GA (FIG. 18). Together, thesefindings show for the first time that RGC-32, FasL, and IL-21 arepotential serum biomarkers of response to GA in multiple sclerosis.

The synchronized changes observed in RGC-32 and FasL mRNA expressionwithin PBMCs either during relapses or with respect to GA therapyresponse may be explained by the known role of RGC-32 in the regulationof FasL expression (Tegla et al., 2013). Since RGC-32 binds to andup-regulates CDC2/cyclin B1 kinase activity (Badea et al., 2002;Fosbrink et al., 2009), FasL expression in T-cells is regulated in partby the CDC2/cyclin B1 complex (Torgler et al., 2004), and RGC-32silencing significantly decreases FasL mRNA expression (Tegla et al.,2013), it is possible that RGC-32 regulates FasL expression bymodulating the activity of the CDC2/cyclin B1 complex. These data alsosuggest that RGC-32 is involved in regulating T-cell apoptosis bymodulating the expression of FasL (Tegla et al., 2013). In MS, myelinand myelin-producing oligodendrocytes in the CNS are targeted forautoimmune attack via antigen-specific CD4+ T cells (Rus et al., 2006).T-cell apoptosis in MS is regulated in part by the Fas-FasL system(Aktas et al., 2006), and ex vivo studies have demonstrated an increasedresistance of T-cells to Fas-mediated apoptosis during MS relapses(Okuda et al., 2006). Thus, in this case a decrease in RGC-32 and anassociated decrease in FasL expression may result in a decrease inFasL-mediated T-cell apoptosis, promote the survival of myelin-targetedT-cells, and result in the onset of clinical relapse and a suboptimalresponse to GA treatment.

It is less clear if and how IL-21 expression is regulated by RGC-32,although IL-21 is involved with T-cell proliferation and cell cycleactivation. Preliminary experiments using CD4+ T-cells from RGC-32knockout mice (Tegla et al., 2015) showed increased expression of IL-21mRNA in the absence of RGC-32 in CD4+ T-cells stimulated withanti-CD3/CD28. These data suggest an inhibitory effect of RGC-32 onIL-21 transcription, which could potentially explain the inverserelationship between RGC-32 and IL-21 mRNA levels as observed in thisstudy. However, further work is needed to confirm these preliminaryresults.

Overall, the data suggest that SIRT1, RGC-32, FasL and IL-21 could serveas serum biomarkers for the detection of MS patient relapse and responseto GA therapy. Such information could potentially help guide treatmentdecisions, delay disease progression, and improve outcomes for MSpatients.

While the invention has been described with reference to certainparticular embodiments thereof, those skilled in the art will appreciatethat various modifications may be made without departing from the spiritand scope of the invention. The scope of the appended claims is not tobe limited to the specific embodiments described.

REFERENCES

All patents and publications mentioned in this specification areindicative of the level of skill of those skilled in the art to whichthe invention pertains. Each cited patent and publication isincorporated herein by reference in its entirety. All of the followingreferences have been cited in this application:

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What is claimed is:
 1. A method for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising (i) determining mRNA expression levels for oneor more biomarkers selected from the group consisting of SIRT1, RGC-32,FasL and IL-21 in a population of cells, (ii) determining mRNAexpression levels for L13 in the same population of cells, and (iii)calculating a ratio of biomarker mRNA expression to L13 mRNA expression,wherein when the biomarker is SIRT1 and the SIRT1/L13 ratio is<3.06±10%, the subject is determined to be undergoing relapse, whereinwhen the biomarker is RGC-32 and the RGC-32/L13 ratio is <1.27±10%, thesubject is determined to be undergoing relapse, wherein when thebiomarker is FasL and the FasL/L13 ratio is <52.6±10%, the subject isdetermined to be undergoing relapse, and wherein when the biomarker isIL-21 and the IL-21/L13 ratio is >16.9±10%, the subject is determined tobe undergoing relapse.
 2. The method of claim 1, wherein when thebiomarker is SIRT1, the SIRT1/L13 ratio is about <3.06.
 3. The method ofclaim 1, wherein when biomarker is RGC-32, the RGC-32/L13 ratio is about<1.27.
 4. The method of claim 1, wherein when the biomarker is FasL, theFasL/L13 ratio is about <52.6.
 5. The method of claim 1, wherein whenthe biomarker is IL-21, the IL-21/L13 ratio is about >16.9.
 6. Themethod of claim 1, wherein mRNA expression levels for one, two, three orfour of the biomarkers are determined.
 7. The method of claim 1, whereinwhen the subject is determined to be undergoing relapse, the methodfurther comprises administering a therapeutically effective amount of atreatment for RRMS to the subject
 8. The method of claim 7, wherein thetreatment is selected from the group consisting of glatiramer acetate(GA), beta-interferons, teriflunomide, fingolimod, dimethyl fumarate,and natalizumab.
 9. The method of claim 1, wherein the population ofcells is selected from the group consisting of peripheral bloodmononuclear cells (PBMCs), CD4+ T cells, CD8+ T cells, MAB328+ cells,GFAP+ cells, leukocytes, monocytes, glial cells, dendritic cells, andneurons.
 10. A method for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) is undergoing relapse ofthe disease, comprising (i) determining protein expression levels forSIRT1 in a population of cells, (ii) determining protein expressionlevels for L13 in the same population of cells, and (iii) calculating aratio of SIRT1 protein expression to L13 protein expression, whereinwhen the SIRT1/L13 ratio is <0.645±10%, the subject is determined to beundergoing relapse.
 11. The method of claim 10, wherein the SIRT1/L13ratio is about <0.645.
 12. The method of claim 10, wherein when thesubject is determined to be undergoing relapse, the method furthercomprises administering a therapeutically effective amount of atreatment for RRMS to the subject
 13. The method of claim 12, whereinthe treatment is selected from the group consisting of glatirameracetate (GA), beta-interferons, teriflunomide, fingolimod, dimethylfumarate, and natalizumab.
 14. The method of claim 10, wherein thepopulation of cells is selected from the group consisting of peripheralblood mononuclear cells (PBMCs), CD4+ T cells, CD8+ T cells, MAB328+cells, GFAP+ cells, leukocytes, monocytes, glial cells, dendritic cells,and neurons.
 15. A method for determining whether a subject havingrelapsing-remitting multiple sclerosis (RRMS) will respond to treatmentwith GA, comprising (i) determining mRNA expression levels for one ormore biomarkers selected from the group consisting of SIRT1, RGC-32,FasL and IL-21 in a population of cells, (ii) determining mRNAexpression levels for L13 in the same population of cells, and (iii)calculating a ratio of biomarker mRNA expression to L13 mRNA expression,wherein when the biomarker is SIRT1 and the SIRT1/L13 ratiois >4.33±10%, it is determined that the subject will respond totreatment with GA, wherein when the biomarker is RGC-32 and theRGC-32/L13 ratio is >2.52±10%, it is determined that the subject willrespond to treatment with GA, wherein when the biomarker is FasL and theFasL/L13 ratio is >85.4±10%, it is determined that the subject willrespond to treatment with GA, and wherein when the biomarker is IL-21and the IL-21/L13 ratio is <11.9±10%, it is determined that the subjectwill respond to treatment with GA.
 16. The method of claim 15, whereinwhen the biomarker is SIRT1, the SIRT1/L13 ratio is about >4.33.
 17. Themethod of claim 15, wherein when biomarker is RGC-32, the RGC-32/L13ratio is about >2.52.
 18. The method of claim 15, wherein when thebiomarker is FasL, the FasL/L13 ratio is about >85.4.
 19. The method ofclaim 15, wherein the biomarker is IL-21, the IL-21/L13 ratio is about<11.9.
 20. The method of claim 15, wherein mRNA expression levels forone, two, three or four of the biomarkers are determined.
 21. The methodof claim 15, wherein when it is determined that the subject will respondto treatment with GA, the method further comprises administering atherapeutically effective amount of GA to the subject.
 22. The method ofclaim 15, wherein when it is determined that the subject will notrespond to treatment with GA, the method further comprises administeringa therapeutically effective amount of non-GA treatment for RRMS.
 23. Themethod of claim 22, wherein the treatment is selected from the groupconsisting of beta-interferons, teriflunomide, fingolimod, dimethylfumarate, and natalizumab.
 24. The method of claim 15, wherein thepopulation of cells is selected from the group consisting of peripheralblood mononuclear cells (PBMCs), CD4+ T cells, CD8+ T cells, MAB328+cells, GFAP+ cells, leukocytes, monocytes, glial cells, dendritic cells,and neurons.